The Site contains a full mountain to sea ecosystem and protects some of the most significant forest area within Palawan Biogeographic Province. Eight forest formations are present: forest over limestone soils, they are composed of species that have adapted to very thin soil such as the Queensland umbrella tree (schefflera) and begonia; montane forest,  of Cleopatra Needle (800-1,500 masl) east of the Park, vegetation is characterized by the growth of mosses, lichens and ferns; forest over ultramafic soil  were vegetation is composed mostly of shrubs and trees growing to a height of not more than 1.5 meters infested with a scrambling bamboo species (Schizostachyum diffusum); lowland evergreen forest include species such as the Dracontomelon dao and Intia bijuga; riverine forest that include species such as the Homonoia riparia ; freshwater swamp forest are composed of tree species adapted to being partly submerged in water for part or most of the year; beach forest  include Calophyllum inophyllum, Pongamia pinnata, and Pandamus sp; and mangrove forest along the Sabang river. Species identified belonged to the Rhizophoraceae family such as Rhizophora spp. and Bruguiera spp.

Flora of the Park represents more than a third of the entire flora of Palawan. At least 800 plant species of plants from 300 genera and 100 families have been identified in the Park. These include at least 295 trees dominated by the dipterocarp species.The diverse species of flora in and around the Park represents a very important gene pool of economically important plant species including rattans (Calamus sp), almaciga (Agathis philippinensis) and rambutan (Nephelium ramboutan-ake).

The faunal diversity in the PPSRNP is moderate with a total of 254terrestrial vertebrate species recorded. A total of 195 species of birds was recorded representing 67% of the total bird species and all of the 15 endemic bird species of Palawan. Notable species include the Blue-headed racquet-tail (Prioniturus platenae), Palawan hornbill (Anthracoceros marchei), Palawan scoops owl (Otus fuliginosus). There are also 30 species of mammals present in the Park. Most common is the long tailed macaque often observed in feeding in the forest canopy and along the shoreline during low tide. Other prominent species are Oriental small-clawed otter (Amblonyx cinereus), Palawan stink badger (Mydaus marchei), and Palawan Arrow-tailed flying squirrel (Hylopetes nigripes). Also notable are 8 species of bats that inhabit the cave. At least 19 species of reptiles have been recorded in the Park, of which 8 species are endemic. Species include large predators like the reticulated python (Python reticulates) and the monitor lizards, also present is the rare fresh water turtles (Caura ambionensis). Important species include the Green sea turtle (Chelonia mydas) and Hawksbill turtle (Eretmochelys imbricate), both internationally endangered species feed on the sea grass beds and nest in the white sand beaches of the St. Paul bay. Amphibians are the smallest group of vertebrates with only 10 species identified. Most dominant and frequently encountered is the Philippine woodland frog (Rana acanthi)

Invertebrate species are principally represented by insect fauna. Of insects surveyed, the Lepidoptera group that include species like butterflies like Trojana .The subterranean river is home to creatures that include Megalomorph spider, Thereupoda, and Amblypygius or tailess whip scorpion.

The marine component is small but important feature of the Site. It includes intertidal zones, seagrass beds, and coral reef. The condition of reefs in St. Paul bay is considered good with more than 57% cover. They are composed primarily of branching table corals with the presence of tabulated, encrusting and massive corals.